Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007035.1 Corchorus olitorius cultivar O-4 contig07060, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 637

Length: 1062
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:213 original size:35 final size:34

Alignment explanation


    Indices: 98--439  Score: 361
    Period size: 35  Copynumber: 9.8  Consensus size: 34

         88 CAAGTTCATA

                          *                     
         98 TTGAAGATGCTACAGCGAGTCATCAT-AA-TCTA-T
          1 TTGAAGATGCTACACCGAGTCATC-TGAATTC-ACT

                         *        *       * *    
        131 TTGAAGATTTGCTGCACCGAGCCCA-CTGAGTCCA-T
          1 TTGAAGA--TGCTACACCGAG-TCATCTGAATTCACT

                  *            *             * 
        166 TATGAATATGCTACACCGATTCATCTGAATTCATT
          1 T-TGAAGATGCTACACCGAGTCATCTGAATTCACT

                                     *  *       
        201 TTGGAAGATGCTACACCGAGTCATCCGAGTTCATCT
          1 TT-GAAGATGCTACACCGAGTCATCTGAATTCA-CT

                                      *        
        237 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ACT

             *                         *    * 
        272 TCGAAGATGCTACACCGAGTCATCTGAGTTCAAT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCACT

                        *               *      *
        306 TTAGAAGATGCTGCACCGAGTCATCTGAGTTCAACC
          1 TT-GAAGATGCTACACCGAGTCATCTGAATTC-ACT

                                      *    *   
        342 TTGAAGATGCTACACCGAGTCATCTGGATTAAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATT-CACT

                                               
        377 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ACT

                                        
        412 TTGAAGATGCTACACCGAGTCATCTGAA
          1 TTGAAGATGCTACACCGAGTCATCTGAA

        440 GATGGTAATG


Statistics
Matches: 260,  Mismatches: 34, Indels: 28
        0.81            0.11        0.09

Matches are distributed among these distances:
  33    9  0.03
  34   22  0.08
  35  214  0.82
  36   15  0.06

ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28


Consensus pattern (34 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCACT

Found at i:436 original size:105 final size:105

Alignment explanation


    Indices: 168--438  Score: 427
    Period size: 105  Copynumber: 2.6  Consensus size: 105

        158 GAGTCCATTA

                *            *             *   *                      *      
        168 TGAATATGCTACACCGATTCATCTGAATTCATTTTGGAAGATGCTACACCGAGTCATCCGAGTTC
          1 TGAAGATGCTACACCGAGTCATCTGAATTCAATTTAGAAGATGCTACACCGAGTCATCTGAGTTC

             * *                              *     
        233 ATCTTTGAAGATGCTACACCGAGTCATCTGGATTCAACTT
         66 AACCTTGAAGATGCTACACCGAGTCATCTGGATTAAACTT

            *                         *                  *                   
        273 CGAAGATGCTACACCGAGTCATCTGAGTTCAATTTAGAAGATGCTGCACCGAGTCATCTGAGTTC
          1 TGAAGATGCTACACCGAGTCATCTGAATTCAATTTAGAAGATGCTACACCGAGTCATCTGAGTTC

                                                    
        338 AACCTTGAAGATGCTACACCGAGTCATCTGGATTAAACTT
         66 AACCTTGAAGATGCTACACCGAGTCATCTGGATTAAACTT

                                                                          
        378 TGAAGATGCTACACCGAGTCATCTGAATTCAACTTT-GAAGATGCTACACCGAGTCATCTGA
          1 TGAAGATGCTACACCGAGTCATCTGAATTCAA-TTTAGAAGATGCTACACCGAGTCATCTGA

        439 AGATGGTAAT


Statistics
Matches: 151,  Mismatches: 14, Indels: 2
        0.90            0.08        0.01

Matches are distributed among these distances:
 105  148  0.98
 106    3  0.02

ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28


Consensus pattern (105 bp):   
TGAAGATGCTACACCGAGTCATCTGAATTCAATTTAGAAGATGCTACACCGAGTCATCTGAGTTC
AACCTTGAAGATGCTACACCGAGTCATCTGGATTAAACTT
Done.